I have a dichotomous variable (0=no ; 1=yes) that I would like to use in a
scatter plot on the y axis as a continuous variable as a % variable.

For example: the x axis could be age and the y axis could be % smokers.

Can anyone help with this ?

You don't say what version of Stata you are using. However, if it is Stata
8, then you can use either -xcollapse- or -xcontract- (downloadable from SSC).

With -xcontract-, you can create a dataset with 1 observation per age group
and smoking category and data on percent of smoking category within age
group, and plot bthe percentages smoking, something like this: